So, you were booked on CX for ICN-HKG-LHR.
The aircraft for ICN-HKG was late, so CX moved you to another airline.
The other airline was late anyway and upon arrival in HKG, CX moved you to the next HKG-LHR flight?

You should get points credited to BA for the HKG-LHR without issue unless CX did something to the FF number when they rebooked you.

Contact BA, tell them what happened and what flights you were booked on and ask for Original Routing Credit.
That should get you points as per what was booked rather then what was flown.